Table 2. Description of proteins in the test set.
| PDB | Resolution (Å) | Protein name | Classification | Protein size (AA) | Host Domain | Insert Domain |
|---|---|---|---|---|---|---|
| 1cip | 1.5 | Guanine nucleotide-binding protein α-1 | Hydrolase | 347 | 32-60; 182-347 | 61-181 |
| 1cjc | 1.7 | Adrenodoxin reductase | Oxidoreductase | 460 | 6-106; 332-460 | 107-331 |
| 1d2k | 2.2 | Chitinase 1 | Hydrolase | 427 | 36-292; 355-427 | 291-354 |
| 1d4d† | 2.5 | Flavocytochrome C fumarate reductase | Oxidoreductase | 569 | 4-359; 506-569 | 360-505 |
| 1d5t* | 1.04 | Guanine nucleotide dissociation inhibitor | Hydrolase inhibitor | 431 | 2-291; 389-431 | 292-388 |
| 1d7l | 2.2 | P-hydroxybenzoate hydroxylase | Oxidoreductase | 394 | 1-173; 276-394 | 174-275 |
| 1dq3 | 2.1 | Endonuclease | Hydrolase | 454 | 1-128; 415-454 | 129-416 |
| 1e1m | 1.85 | Adrenodoxin reductase | Oxidoreductase | 460 | 6-106; 332-460 | 107-331 |
| 1edq† | 1.55 | Chitinase A | Hydrolase | 563 | 24-443; 517-563 | 444-516 |
| 1el5* | 1.8 | Sarcosine oxidase | Oxidoreductase | 385 | 1-217; 322-385 | 218-321 |
| 1fcf | 2.1 | Photosystem II D1 protease | Hydrolase | 463 | 77-156; 249-463 | 157-248 |
| 1fl2 | 1.9 | Alkyl hydroperoxide reductase subunit F | Oxidoreductase | 521 | 212-325; 452-521 | 326-451 |
| 1gcu* | 1.4 | Biliverdin reductase A | Oxidoreductase | 292 | 1-128; 247-292 | 129-246 |
| 1h3n† | 2 | Leucyl-tRNA synthetase | Aminoacyl-trna synthetase | 813 | 1-225; 418-813 | 226-417 |
| 1hkk | 1.85 | Chitotriosidase | Hydrolase | 385 | 22-266; 335-385 | 267-334 |
| 1hku | 2.3 | C-Terminal binding protein 3 | Transcription co-repressor | 345 | 15-114; 308-345 | 115-307 |
| 1ile† | 2.5 | Isoleucyl-tRNA synthetase | Aminoacyl-trna synthetase | 821 | 1-197; 387-821 | 198-386 |
| 1itx | 1.1 | Glycosyl hydrolase | Hydrolase | 451 | 33-337; 410-451 | 338-409 |
| 1iz0 | 2.3 | Quinone oxidoreductase | Oxidoreductase | 301 | 2-98; 270-302 | 99-269 |
| 1jnd | 1.3 | Imaginal disc growth factor-2 | Hormone/growth factor | 420 | 2-278; 371-420 | 279-370 |
| 1k0i* | 1.8 | P-Hydroxybenzoate hydroxylase | Hydrolase | 394 | 1-173; 276-394 | 174-275 |
| 1kfw | 1.74 | Chitinase B | Hydrolase | 444 | 10-327; 389-444 | 328-388 |
| 1kit† | 2.3 | Sialidase | Hydrolase | 781 | 25-216; 347-781 | 217-346 |
| 1l6j† | 2.5 | Matrix metalloproteinase-9 | Hydrolase | 444 | 29-215; 391-444 | 216-390 |
| 1lfw | 1.8 | PepV | Hydrolase | 468 | 1-186; 383-468 | 187-382 |
| 1lrz | 2.1 | Factor essential for expression of methicillin | Antibiotic inhibitor | 412 | 1-244; 310-412 | 245-309 |
| 1m1h | 1.95 | Transcription antitermination protein NusG | Transcription | 186 | 5-50; 132-186 | 51-131 |
| 1m6i | 1.8 | Programmed cell death protein 8 | Oxidoreductase | 608 | 128-263; 401-477 | 264-400 |
| 1mla* | 1.5 | Malonyl-coenzyme A acyl carrier protein | Acyltransferase | 307 | 3-127; 198-307 | 128-198 |
| 1mx3 | 1.95 | C-terminal binding protein 1 | Transcription repressor | 352 | 27-125; 319-352 | 126-318 |
| 1nhq | 2 | C-terminal binding protein 1 | Oxidoreductase | 321 | 1-119; 243-321 | 120-242 |
| 1nof | 1.42 | Xylanase | Hydrolase | 413 | 31-43; 321-413 | 44-320 |
| 1npx | 2.16 | Xylanase | Oxidoreductase | 321 | 1-119; 243-321 | 120-242 |
| 1nx6 | 2.15 | Aspartate-semialdehyde dehydrogenase | Oxidoreductase | 371 | 1-133; 358-371 | 134-357 |
| 1owq | 2 | Signal processing protein | Signaling protein | 361 | 1-239; 308-361 | 240-307 |
| 1p1m | 1.5 | Hypothetical protein TM0936 | Unkown function | 404 | 1-49; 331-404 | 50-330 |
| 1ps9† | 2.2 | 2,4-dienoyl-CoA reductase | Oxidoreductase | 671 | 1-465; 628-671 | 466-627 |
| 1qjd† | 1.8 | Flavocytochrome C3 | Fumarate reductase | 568 | 1-359; 506-568 | 360-505 |
| 1qmh* | 2.1 | Rna 3′-terminal phosphate cyclase | Phosphate cyclase | 338 | 5-184; 280-338 | 185-279 |
| 1tf5† | 2.18 | Preprotein translocase seca subunit | Protein transport | 780 | 1-226; 349-780 | 227-348 |
| 1uj4 | 1.8 | Ribose 5-phosphate isomerase | Isomerase | 227 | 3-131; 206-227 | 132-205 |
| 1uuf | 1.76 | Zinc-type alcohol dehydrogenase-like protein | Oxidoreductase | 348 | 3-144; 313-348 | 145-312 |
| 1vhe | 1.9 | Aminopeptidase/glucanase homolog | Unkown function | 367 | 3-72; 163-367 | 73-162 |
| 1vho | 1.86 | Endoglucanase | Unkown function | 333 | 3-69; 153-333 | 70-152 |
| 1vj1 | 2.1 | Putative NADPH-dependent oxidoreductase | Unknown function | 351 | 1-124; 312-351 | 125-311 |
| 1w0o† | 1.9 | Sialidase | Hydrolase | 777 | 25-216; 347-777 | 217-346 |
| 1w6k | 2.1 | Lanosterol synthase | Isomerase | 732 | 6-99; 379-732 | 100-378 |
| 1xgs* | 1.75 | Methionine aminopeptidase | Aminopeptidase | 295 | 1-194; 272-295 | 195-271 |
| 1xhc | 2.35 | NADH oxidase /Nitrite reductase | Oxidoreductase | 289 | 1-103; 226-289 | 104-225 |
| 1xmb | 2 | IAA-amino acid hydrolase homolog 2 | Hydrolase | 407 | 16-194; 314-407 | 195-313 |
*
Indicates a protein is part of the development set
†
Indicates the “host domain” includes more than one structural domain. Additional domains are as follows: 1d4d, 4-102; 1edq, 24-132; 1h3n, 687-814; 1ile, 682-821; 1kit, 544-781; 1l6j, 29-105; 1ps9, 1-330; 1qjd, 1-102; 1tf5, 571-780; 1w0o, 544-777.